#!/bin/sh
hadoop fs -rmr /user/aaithal/indel/output/cleanup/
hadoop jar /usr/lib/hadoop/contrib/streaming/hadoop-streaming-0.20.2+737.jar -input /user/aaithal/input/indel/ecoli/partial/1 -output /user/aaithal/indel/output/cleanup/ -mapper cleanup.pl -file cleanup.pl -jobconf mapred.map.tasks=10 -jobconf mapred.reduce.tasks=10 -jobconf name=ind
hadoop fs -rmr  /user/aaithal/output/indel/ecoli/partial/1
hadoop jar /usr/lib/hadoop/contrib/streaming/hadoop-streaming-0.20.2+737.jar -input /user/aaithal/input/indel/ecoli/partial/1 -output /user/aaithal/output/indel/ecoli/partial/1 -mapper wrap_align.pl -file wrap_align.pl -jobconf mapred.map.tasks=10 -jobconf mapred.reduce.tasks=10 -jobconf name=inde



hadoop fs -rmr /user/aaithal/indel/output/cleanup/
hadoop jar /usr/lib/hadoop/contrib/streaming/hadoop-streaming-0.20.2+737.jar -input /user/aaithal/indel/input/ -output /user/aaithal/indel/output/cleanup/ -mapper cleanup.pl -file cleanup.pl -jobconf mapred.map.tasks=10 -jobconf mapred.reduce.tasks=10 -jobconf name=ind
hadoop fs -rmr /user/aaithal/output/indel/ecoli/partial/2
hadoop jar /usr/lib/hadoop/contrib/streaming/hadoop-streaming-0.20.2+737.jar -input /user/aaithal/output/indel/ecoli/partial/1 -output /user/aaithal/output/indel/ecoli/partial/2 -mapper wrap_sam.pl -file wrap_sam.pl -jobconf mapred.map.tasks=10 -jobconf mapred.reduce.tasks=1 -partitioner org.apache.hadoop.mapred.lib.KeyFieldBasedPartitioner -jobconf mapred.output.key.comparator.class=org.apache.hadoop.mapred.lib.KeyFieldBasedComparator -jobconf stream.num.map.output.key.fields=2 -jobconf mapred.text.key.partitioner.options=-k1,2n -jobconf mapred.text.key.comparator.options=-k2,2n
#-reducer wrap_pileup.pl -file wrap_pileup.pl -jobconf mapred.map.tasks=400 -jobconf mapred.reduce.tasks=1 -jobconf name=inde #-partitioner org.apache.hadoop.mapred.lib.KeyFieldBasedPartitioner -jobconf mapred.output.key.comparator.class=org.apache.hadoop.mapred.lib.KeyFieldBasedComparator -jobconf stream.map.output.field.separator=delim -jobconf stream.num.map.output.key.fields=1 -jobconf map.output.key.field.separator=delim -jobconf mapred.text.key.partitioner.options=-k1,1 
